Define where the pipeline should find input data and save output data.

Path to tab-separated sample sheet

required
type: string

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Parameters for QC and trim short-reads

save files that failed to pass trimming thresholds ending in *.fail.fastq.gz

type: boolean

save all merged reads to the a file ending in *.merged.fastq.gz

type: boolean

Skip FastQC

type: boolean

Skip FastP

type: boolean

Path to Kraken2 database.

type: string

Parameters for the assembly

The assembler to use for assembly. Use the appropriate assembler according to the chosen assembly_type. Refer to the README.md for further clarification.

type: string

Which type of assembly to perform.

type: string

Extra arguments for Unicycler

type: string

Allowed technologies for long read assembly.

type: string

This can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.

type: string

Extra arguments for Dragonflye

type: string

Which assembly polishing method to use.

type: string

Parameters for the annotation

The annotation method to annotate the final assembly.

type: string

Extra arguments for prokka annotation tool.

type: string

Path to Bakta database

type: string

Download Bakta database

type: boolean

This can be used to supply extra options to the Bakta download module

type: string

Specifies a configuration file for the DFAST annotation method.

type: string
default: assets/test_config_dfast.py

Skip running Kraken2 classifier on reads.

type: boolean

Skip annotating the assembly with Prokka /DFAST.

type: boolean

Skip running PycoQC on long read input.

type: boolean

Skip polishing the long-read assembly with fast5 input. Will not affect short/hybrid assemblies.

type: boolean

Skip MultiQC

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean

A comma separated string of inputs the schema validation should ignore

hidden
type: string
default: modules,igenomes_base